mmg_233_2013_genetics_genomicswikiaorg-20200214-history
OMIM: Online Mendelian Inheritance in Man
The database "Online Mendelian Inheritance in Man" or OMIM, is a collection of diseases observed to be Mendelian, or inherited from parent to child among families. The database contains 14,359 (as of September 06, 2013) genes that have been linked to mendelian genetic disorders. In addition to information on genetic disorders, the database contains external links to other databases such as NCBI Homologene and Reactome for searching any genetic homologues to or cellular pathways involved with the gene in question (1). Currently, OMIM is managed by Dr. Ada Homash from Johns Hopkins University, and is a collaboration between Johns Hopkins, the McKusik-Nathans Institute of Genetic Medicine, and the National Human Genome Research Institute. History of OMIM OMIM originally began as a written compilation of notes by Dr. Victor McKusick (1921-2008), who is remembered as the "Father of Medical Genetics " (Figure 1) (2). Every time Dr. McKusick came across a new phenotype, he cataloged it in a notebook. The first edition of Mendelian Inheritance in Man ''(MIM) was published in 1966. In 1987, the collection was made available over the internet and NCBI developed the catalog for the web in 1995. MIM is no longer in print (volume 12 was published in 1998) (1,2). Medical professionals and scientists are encouraged to submit new mendelian disorder phenotypes and the genes responsible to OMIM. Using OMIM OMIM is used as an information database about mendelian genetic disorders. In the search bar from the main homepage, one can enter the name of a disease (Figure 2), a disease symptom (Figure 3), or the gene thought to be involved (Figure 4). Each figure 2-4 describes the disease, a symptom, and gene involved with Marfan syndrome, a disease characterized by poor generation of connective tissue (3). Each search criteria returned the same "Marfan Syndrome" information page with detailed information from published scientific articles. If an associated gene is found, one can use the External Links to access other databases about the same gene (Figures 5-6). For example, on the fibrillin-1 page (the gene mutated in Marfan Syndrome), one can click the link to Ensembl (Figure 6), which opens a page with the gene mapping information on ''FBN-1 . In this way, OMIM can be used for a myriad of information on Mendelian disorders. Marfan 2.png|Figure 2. Using OMIM. OMIM can be used to look-up information on a particular genetic disorder. Here, Marfan Syndrome is entered and the pages returned have all been implicated in this disease. Marfan 3.png|Figure 3. Entering known symptom into OMIM. If a particular symptom of a disease is known, it can be entered. As noted here, "aortic aneurysm" is a symptom for Marfan Syndrome. Marfan 4.png|Figure 4. Entering a gene into OMIM. Third, if a gene has been implicated in a disorder, that gene can be entered. Here, fibrillin-1 has been entered and returned Marfan syndrome. Marfan 5.png|Figure 5. External Links. OMIM contains external links to the genes and symptoms searched. When in an information page, any link can be used, taking the reader to that database's information page of that gene. Here, Ensembl was clicked. Marfan 6.png|Figure 6. Connect to External Links. In OMIM, Fibrillin-1 was searched for (Figure 4). Then the external link to Ensembl used, and the reader was redirected to the Ensembl FBN-1 gene. OMIM as a Resource OMIM is not just a public information database, but also a vast databank that can be mined for use in genetic association studies (4 ), genetic variation (5 ), and for studying single nucleotide polymorphisms in disease (6 ). In a genetic association study, Chen et al. divised a way to link OMIM disease to microRNAs, in order to better understand the diseases in question. The authors used a "random walk " model and determined the probability that a known "seed" or already associated OMIM disease and microRNA would reach a random unknown node. If the probability was high, that disease was considered to be associated. Using this method, phenotypically similar diseases were found to be associated with the same microRNA (4). Peterson et al. wrote a review analyzing the information in OMIM and other databases like it, discussing the potential to use this information in personalized medicine. The authors discuss the advantages and challenges of such large information databases and the best ways to mine the data for human variants of genetic disease (5). In a third study using OMIM, Yang et al. wanted to integrate disease and single nucleotide polymorphisms (SNPs) that are associated with disease into one database. At the time of the paper (2008) this information had not been integrated (6). Additionally, Hijikata et al. ''used the OMIM database to map genetic mutations associated with genetic disease (7 ). These studies suggest that OMIM can be used as knowledge base and data mining tool to study genetic association, variation, and mutation to any of the diseases currently cataloged in the OMIM database. References 1. Online Mendelian Inheritance in Man. Updated Daily. www.omim.org 2. National Library of Medicine. Profiles in Science: The Victor A. McKusick Papers. http://profiles.nlm.nih.gov/ps/retrieve/Collection/CID/JQ 3. OMIM. ''Marfan Syndrome. #154700; Fibrillin-1. #134797 4. Chen H and Zhang Z. Prediction of associations between OMIM diseases and microRNAs by random walk on OMIM disease similarity network. Scientific World Journal. 2013 Epub. Mar 20 PMID: 23576899 5. Peterson et al. Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants. J Mol Biol. (2013). August 17. pii: S0022-2836(14)00511-1. PMID: 23962656 6. Yang JO et al. An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. BMC Bioinformatics. (2008). Dec 12; 9 Suppl 12:S19. PMID: 19091018 7. Hijikata et al. Mutation@A Glance: An Integrative Web Application for Analysing Mutations from Human Genetic Diseases. Published online 2010 April 1. PMCID: PMC2638159